LALIGN/PLALIGN(1) LALIGN/PLALIGN(1)NAMElalign - compare two protein or DNA sequences for local similarity and
show the local sequence alignments
plalign,flalign - compare two sequences for local similarity and plot
the local sequence alignments
SYNOPSISlalign [-EKfgiImnNOQqrRswxZ] sequence-file-1 sequence-file-2
plalign [-EKfgiImnNQqrRsvwxZ] sequence-file-1 sequence-file-2
DESCRIPTIONlalign and plalign programs compare two sequences looking for local
sequence similarities. lalign/plalign use code developed by X. Huang
and W. Miller (Adv. Appl. Math. (1991) 12:337-357) for the "sim" pro‐
gram. (Version 2.1 uses sim2 code.) While ssearch reports only the
best alignment between the query sequence and the library sequence,
lalign and plalign will report all the alignments with pair-wisse prob‐
abilities < 0.05 (default, modified with -E #) between the two
sequences lalign shows the actual local alignments between the two
sequences and their scores, while plalign produces a plot of the align‐
ments that looks similar to a `dot-matrix' homology plot. On Unix™
systems, plalign generates postscript output. flalign generates
graphic commands for the GCG "figure" program.
Probability estimates for the lalign/plalign/flalign programs are based
on the parameters provided by Altschul and Gish (1996) Meth. Enzymol.
266:460-480. These parameters are available for BLOSUM50, BLOSUM62,
and PAM250 scoring matrices with specific gap penalties, and also for
DNA comparison with a gap penalty of -16, -4. Probability estimates
are not available for other scoring matrices and gap penalties.
The E(10,000) values reported with the alignments are the pairwise-
alignment probabilities multiplied by 10,000. These estimates approxi‐
mate the significance from a search of a 10,000 entry database. They
differ from the -E 0.05 initial theshold by the same factor of 10,000.
This is an unfortunate inconsistency, but I believe that it is helpful
to provide the perspective of a database search.
The lalign/plalign/fasta programs use a standard text format sequence
file. Lines beginning with '>' or ';' are considered comments and
ignored; sequences can be upper or lower case, blanks,tabs and unrecog‐
nizable characters are ignored. lalign/plalign expect sequences to use
the single letter amino acid codes, see protcodes(1) .
OPTIONSlalign and the other programs can be directed to change the scoring
matrix, search parameters, output format, and default search directo‐
ries by entering options on the command line (preceeded by a `-'). All
of the options should preceed the file name and ktup arguments). Alter‐
nately, these options can be changed by setting environment variables.
The options and environment variables are:
-E # Pairwise-probability limit (default -E 0.05).
-K # maximum number of alignments to be shown (default -K 50).
-f # Penalty for the first residue a gap (-14 by default).
-g # Penalty for each additional residue in a gap (-4 by default).
-i Compare the reverse complement (DNA only).
-I Show alignment between identical sequences. Normally, the iden‐
tity alignment is not shown.
-m # (MARKX) =1,2,3. Alternate display of matches and mismatches in
alignments. MARKX=1 uses ":","."," ", for identities, conseva‐
tive replacements, and non-conservative replacements, respec‐
tively. MARKX=2 uses " ","x", and "X". MARKX=3 does not show
the second sequence, but uses the second alignment line to dis‐
play matches with a "." for identity, or with the mismatched
residue for mismatches. MARKX=3 is useful for aligning large
numbers of similar sequences.
-n pre-specify DNA sequence, rather than infer from sequence.
-N # limit first and second sequences to '#' residues.
-s str (SMATRIX) the filename of an alternative scoring matrix file.
For protein sequences, BLOSUM50 is used by default; PAM250 can
be used with the command line option -s P250, BLOSUM62 with "-s
BL62".
-v str (LINEVAL) (plalign only) plalign can use up to 4 different line
styles to denote the scores of local alignments. The scores
that correspond to these line styles can be specified with the
environment variable LINVAL, or with the -v option. In either
case, a string with three numbers separated by spaces should be
given. This string must be surrounded by double quotation
marks. For example, LINEVAL="200 100 50" tells plalign to use
solid lines for local alignments with scores greater than 200,
long dashed lines for scores between 100 and 200, short dashed
lines for scores between 50 and 100, and dotted lines for scores
less than 50.
plalign -v "200 100 50"
Normally, the values are 200, 100, and 50 for protein sequence
comparisons and 400, 200, and 100 for DNA sequence comparisons.
-w # (LINLEN) output line length for sequence alignments. (normally
60, can be set up to 200).
EXAMPLES
(1) lalign mchu.aa mchu.aa
Compare the amino acid sequence in the file mchu.aa with itself and
report the ten best local alignments. Sequence files should have the
form:
>MCHU - Calmodulin - Human ...
ADQLTEEQIAEF ...
(2) plalign -K 100 -E 0.01 qrhuld.aa egmsmg.aa
Display up to 100 local alignments of the LDL receptor (qrhuld.aa) with
epidermal growth factor precursor (egmsmg.aa) with pairwise probabili‐
ties better than 0.01. Plot the results on the screen.
(3) lalign
Run the lalign program in interactive mode. The program will prompt
for the name of two sequence files and the number of alignments to
show.
SEE ALSOssearch(1), prss(1), fasta(1), protcodes(5), dnacodes(5)AUTHOR
Bill Pearson
wrp@virginia.EDU
local LALIGN/PLALIGN(1)
